INCLUDES=-I$(top_srcdir)/src/include/sparsehash -I$(top_srcdir)/src/include/sparsehash/linux \
-I$(top_srcdir)/src/include/logging

# The libraries libglog depends on.
#COMMON_LIBS = $(PTHREAD_LIBS) $(GFLAGS_LIBS) $(UNWIND_LIBS)

bindir=`pwd`/../bin
bin_PROGRAMS=SeqAsm
SeqAsm_SOURCES=DeBruijnGraphBuilder.cpp  Global.cpp \
DeBruijnGraphBuilder.h    Global.h                  SparseMapWrapper.h\
DeBruijnGraph.cpp         GraphErrorCorrector.cpp   HashTree.h\
DeBruijnGraph.h           GraphErrorCorrector.h     array.h\
GraphExaminator.h         BitDeque.h				BinarySearchArray.h\
Disambiguation.cpp        ReadInputFacts.h 			BinarySearchMap.h\
Disambiguation.h          IntervalList.cpp          run.cpp \
FastaReader.cpp           IntervalList.h            SequenceGraph.cpp \
FastaReader.h             KmerCounter.cpp           SequenceGraph.h \
fib.c                     KmerCounter.h             stdio64.h\
fib.h                     Kmer.cpp                  DissectBubblesCorrector.h ReadInputFacts.h			FixedHashTree.h			  MemoryPool.h\
FibHeap.h                 Kmer.h                    DissectBubblesCorrector.cpp\
fibpriv.h                 Splay.h					SplayMap.h\
SequenceGraphViz.h        SequenceGraphViz.cpp		SplaySet.h\
map_utility.h
SeqAsm_LDADD = include/logging/libglog.la
SeqAsm_LDFLAGS= -static include/logging/libglog.la -D_GNU_SOURCE $(PTHREAD_CFLAGS)
SeqAsm_CXXFLAGS = $(PTHREAD_CFLAGS)

DEFS+=-D_GNU_SOURCE

